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Log of ./fah6
Mon Aug 17 19:05:11 2009
Note: Please read the license agreement (fah6 -license). Further
use of this software requires that you have read and accepted this agreement.
2 cores detected
--- Opening Log file [August 17 17:05:11 UTC]
# Linux SMP Console Edition ###################################################
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Folding@Home Client Version 6.24beta
http://folding.stanford.edu
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Launch directory: /home/slls/folding
Executable: ./fah6
Arguments: -smp -forceasm -verbosity 9 -advmethods
[17:05:11] - Ask before connecting: No
[17:05:11] - User name: ^w^ing (Team 0)
[17:05:11] - User ID: 5D0A6C315E038214
[17:05:11] - Machine ID: 16
[17:05:11]
[17:05:11] Loaded queue successfully.
[17:05:11] - Autosending finished units... [August 17 17:05:11 UTC]
[17:05:11] Trying to send all finished work units
[17:05:11] + No unsent completed units remaining.
[17:05:11] - Autosend completed
[17:05:11]
[17:05:11] + Processing work unit
[17:05:11] At least 4 processors must be requested.Core required: FahCore_a2.exe
[17:05:11] Core found.
[17:05:11] Working on queue slot 07 [August 17 17:05:11 UTC]
[17:05:11] + Working ...
[17:05:11] - Calling './mpiexec -np 4 -host 127.0.0.1 ./FahCore_a2.exe -dir work/ -suffix 07 -checkpoint 30 -forceasm -verbose -lifeline 4541 -version 624'
[17:05:11]
[17:05:11] *------------------------------*
[17:05:11] Folding@Home Gromacs SMP Core
[17:05:11] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[17:05:12]
[17:05:12] Preparing to commence simulation
[17:05:12] - Ensuring status. Please wait.
[17:05:21] - Assembly optimizations manually forced on.
[17:05:21] - Not checking prior termination.
[17:05:29] - Expanded 1502956 -> 24031357 (decompressed 1598.9 percent)
[17:05:35] Called DecompressByteArray: compressed_data_size=1502956 data_size=24031357, decompressed_data_size=24031357 diff=0
[17:05:35] - Digital signature verified
[17:05:35]
[17:05:35] Project: 2677 (Run 19, Clone 97, Gen 30)
[17:05:35]
[17:05:36] Assembly optimizations on if available.
[17:05:36] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=ubuntu
NNODES=4, MYRANK=3, HOSTNAME=ubuntu
NNODES=4, MYRANK=2, HOSTNAME=ubuntu
NNODES=4, MYRANK=1, HOSTNAME=ubuntu
NODEID=0 argc=20
NODEID=1 argc=20
NODEID=3 argc=20
NODEID=2 argc=20
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.99_development_20090307 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
:-) mdrun (-:
Reading file work/wudata_07.tpr, VERSION 3.3.99_development_20070618 (single precision)
Note: tpx file_version 48, software version 64
NOTE: The tpr file used for this simulation is in an old format, for less memory usage and possibly more performance create a new tpr file with an up to date version of grompp
Making 1D domain decomposition 1 x 1 x 4
starting mdrun '22869 system in water'
7750000 steps, 15500.0 ps (continuing from step 7500000, 15000.0 ps).
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483269. It should have been within [ 0 .. 9464 ]
For more information and tips for trouble shooting please check the GROMACS Wiki at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: nsgrid.c, line: 357
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483611. It should have been within [ 0 .. 256 ]
For more information and tips for trouble shooting please check the GROMACS Wiki at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 3, will try to stop all the nodes
Halting parallel program mdrun on CPU 3 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_3]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 4
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0Edited title to add "one core issue" -- susato